1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
|
\name{root}
\alias{root}
\alias{root.phylo}
\alias{root.multiPhylo}
\alias{unroot}
\alias{unroot.phylo}
\alias{unroot.multiPhylo}
\alias{is.rooted}
\alias{is.rooted.phylo}
\alias{is.rooted.multiPhylo}
\title{Roots Phylogenetic Trees}
\description{
\code{root} reroots a phylogenetic tree with respect to the specified
outgroup or at the node specified in \code{node}.
\code{unroot} unroots a phylogenetic tree, or returns it unchanged if
it is already unrooted.
\code{is.rooted} tests whether a tree is rooted.
}
\usage{
root(phy, ...)
\method{root}{phylo}(phy, outgroup, node = NULL, resolve.root = FALSE,
interactive = FALSE, edgelabel = FALSE, ...)
\method{root}{multiPhylo}(phy, outgroup, ...)
unroot(phy)
\method{unroot}{phylo}(phy)
\method{unroot}{multiPhylo}(phy)
is.rooted(phy)
\method{is.rooted}{phylo}(phy)
\method{is.rooted}{multiPhylo}(phy)
}
\arguments{
\item{phy}{an object of class \code{"phylo"} or \code{"multiPhylo"}.}
\item{outgroup}{a vector of mode numeric or character specifying the
new outgroup.}
\item{node}{alternatively, a node number where to root the tree.}
\item{resolve.root}{a logical specifying whether to resolve the new
root as a bifurcating node.}
\item{interactive}{if \code{TRUE} the user is asked to select the node
by clicking on the tree which must be plotted.}
\item{edgelabel}{a logical value specifying whether to treat node
labels as edge labels and thus eventually switching them so that
they are associated with the correct edges when using
\code{\link{drawSupportOnEdges}} (see Czech et al. 2016).}
\item{\dots}{arguments passed among methods (e.g., when rooting lists
of trees).}
}
\details{
The argument \code{outgroup} can be either character or numeric. In
the first case, it gives the labels of the tips of the new outgroup;
in the second case the numbers of these labels in the vector
\code{phy$tip.label} are given.
If \code{outgroup} is of length one (i.e., a single value), then the
tree is rerooted using the node below this tip as the new root.
If \code{outgroup} is of length two or more, the most recent common
ancestor (MRCA) \emph{of the ingroup} is used as the new root. Note
that the tree is unrooted before being rerooted, so that if
\code{outgroup} is already the outgroup, then the returned tree is not
the same than the original one (see examples). If \code{outgroup} is
not monophyletic, the operation fails and an error message is issued.
If \code{resolve.root = TRUE}, \code{root} adds a zero-length branch
below the MRCA of the ingroup.
A tree is considered rooted if either only two branches connect to the
root, or if there is a \code{root.edge} element. In all other cases,
\code{is.rooted} returns \code{FALSE}.
}
\note{
The use of \code{resolve.root = TRUE} together with \code{node = }
gives an error if the specified node is the current root of the
tree. This is because there is an ambiguity when resolving a node in
an unrooted tree with no explicit outgroup. If the node is not the
current root, the ambiguity is solved arbitrarily by considering the
clade on the right of \code{node} (when the tree is plotted by
default) as the ingroup. See a detailed explanation there:
\url{https://www.mail-archive.com/r-sig-phylo@r-project.org/msg03805.html}.
}
\value{
an object of class \code{"phylo"} or \code{"multiPhylo"} for
\code{root} and \code{unroot}; a logical vector for \code{is.rooted}.
}
\references{
Czech, L., Huerta-Cepas, J. and Stamatakis, A. (2017) A critical
review on the use of support values in tree viewers and bioinformatics
toolkits. \emph{Molecular Biology and Evolution}, \bold{34},
1535--1542. \doi{10.1093/molbev/msx055}
}
\author{Emmanuel Paradis}
\seealso{
\code{\link{bind.tree}}, \code{\link{drop.tip}},
\code{\link{nodelabels}}, \code{\link{identify.phylo}}
}
\examples{
data(bird.orders)
plot(root(bird.orders, 1))
plot(root(bird.orders, 1:5))
tr <- root(bird.orders, 1)
is.rooted(bird.orders) # yes
is.rooted(tr) # no
### This is because the tree has been unrooted first before rerooting.
### You can delete the outgroup...
is.rooted(drop.tip(tr, "Struthioniformes"))
### ... or resolve the basal trichotomy in two ways:
is.rooted(multi2di(tr))
is.rooted(root(bird.orders, 1, r = TRUE))
### To keep the basal trichotomy but forcing the tree as rooted:
tr$root.edge <- 0
is.rooted(tr)
x <- setNames(rmtree(10, 10), LETTERS[1:10])
is.rooted(x)
}
\keyword{manip}
|
